ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser.java Source code

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Here is the source code for ubic.gemma.core.loader.entrez.pubmed.ESearchXMLParser.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2006 University of British Columbia
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
package ubic.gemma.core.loader.entrez.pubmed;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;

import ubic.gemma.core.util.XMLUtils;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.io.InputStream;
import java.util.Collection;
import java.util.HashSet;

/**
 * @author pavlidis
 */
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
public class ESearchXMLParser {

    private static final Log log = LogFactory.getLog(ESearchXMLParser.class);

    public Collection<String> parse(InputStream is) throws IOException, ParserConfigurationException, SAXException {
        Document document = this.openAndParse(is);
        return this.extractIds(document);
    }

    public int getCount(InputStream is) throws IOException, ParserConfigurationException, SAXException {
        Document document = this.openAndParse(is);
        NodeList idList = document.getElementsByTagName("Count");
        Node item = idList.item(0);
        String value = XMLUtils.getTextValue((Element) item);
        ESearchXMLParser.log.debug("Got " + value);
        return Integer.parseInt(value);
    }

    private Document openAndParse(InputStream is) throws IOException, ParserConfigurationException, SAXException {
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        factory.setIgnoringComments(true);

        DocumentBuilder builder = factory.newDocumentBuilder();
        return builder.parse(is);
    }

    private Collection<String> extractIds(Document doc) {
        Collection<String> result = new HashSet<>();
        NodeList idList = doc.getElementsByTagName("Id");
        assert idList != null;
        ESearchXMLParser.log.debug("Got " + idList.getLength());

        for (int i = 0; i < idList.getLength(); i++) {
            Node item = idList.item(i);
            String value = XMLUtils.getTextValue((Element) item);
            ESearchXMLParser.log.debug("Got " + value);
            result.add(value);
        }

        return result;
    }

}